Contacts of the helix formed by residues 276 - 281 (chain G) in PDB entry 2QJK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 276 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147G TYR* 3.6 21.7 + - - +
154G MET* 3.7 21.5 - - + -
275G GLY* 1.3 70.5 - - - -
277G PRO* 1.3 60.1 - - + +
278G ASP* 2.8 68.1 + - + +
279G ASN* 2.8 22.5 + - - +
280G TYR* 5.0 3.5 - - - -
291G HIS* 3.0 30.3 + - + +
293G VAL* 3.8 23.2 - - + +
294G PRO 5.7 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 277 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272G ASN 5.8 1.3 - - - +
275G GLY 3.1 12.3 - - - +
276G HIS* 1.3 91.4 - - + +
278G ASP* 1.3 64.3 + - - +
279G ASN 3.2 1.8 + - - -
280G TYR* 3.4 14.3 + - + +
105H LYS 3.9 11.0 - - - +
106H ALA* 3.2 43.0 - - - +
107H ARG* 4.3 3.8 - - - +
108H ALA* 4.5 10.8 - - + +
120H GLN* 5.4 2.7 - - - +
125H ILE* 4.3 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 278 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153G GLN* 3.3 13.6 - - + +
154G MET* 3.6 16.2 - - + -
276G HIS* 2.8 32.3 + - + +
277G PRO* 1.3 78.1 - - - +
279G ASN* 1.3 56.4 + - - +
280G TYR 3.1 5.8 - - - -
281G ILE* 3.1 33.8 + - + +
289G PRO* 3.0 28.0 - - - +
291G HIS* 4.6 9.0 + - - +
106H ALA 4.2 7.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 279 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G PHE* 3.7 15.2 - - - -
94G ARG* 5.4 4.0 + - - +
147G TYR* 3.5 34.6 + - + +
150G PRO* 4.6 11.4 - - - +
152G GLY* 3.0 13.2 - - - -
153G GLN 4.2 0.2 - - - +
154G MET* 3.0 29.0 + - + +
155G SER* 2.9 26.7 + - - -
276G HIS 2.8 14.3 + - - +
278G ASP* 1.3 75.8 - - - +
280G TYR* 1.3 62.6 + - + +
281G ILE 3.0 7.6 + - - +
502G HEM 5.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 280 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G PHE* 3.8 10.9 - + - -
81G GLU* 4.6 2.9 - - - -
94G ARG* 4.3 26.0 + - - -
95G TYR* 3.6 9.4 + - - -
272G ASN* 2.5 30.7 + - + -
276G HIS 5.0 3.1 - - - -
277G PRO* 3.4 16.5 + - + +
278G ASP 3.1 1.8 - - - -
279G ASN* 1.3 81.7 - - + +
281G ILE* 1.3 62.2 + - - +
282G GLU 4.2 0.2 + - - -
102H LEU* 3.5 47.8 - - + +
105H LYS* 3.0 63.9 + - + -
106H ALA* 4.0 12.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 281 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77G PHE* 4.4 1.3 - - - -
152G GLY* 3.2 6.3 - - - -
153G GLN* 2.9 43.7 + - + +
278G ASP* 3.1 29.2 - - + +
280G TYR* 1.3 84.0 - - - +
282G GLU* 1.3 71.5 + - - +
284G ASN* 6.0 0.2 - - + -
103H MET* 6.3 0.4 - - + -
106H ALA* 4.2 13.2 - - + +
107H ARG* 3.5 28.3 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il